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publications
Therapeutic target database update 2016: enriched resource for bench to clinical drug target and targeted pathway information
Published in Nucleic Acids Research, 2016
This paper details a major update to the Therapeutic Target Database (TTD), significantly increasing its coverage of clinical trial drugs and targets, and cross-linking them to major pathway databases.
Recommended citation: Yang, H., Qin, C., Li, Y. H., Tao, L., Zhou, J., Yu, C. Y., Xu, F., Chen, Z., Zhu, F., & Chen, Y. Z. (2016). "Therapeutic target database update 2016: enriched resource for bench to clinical drug target and targeted pathway information." Nucleic Acids Research. 44(D1):D1069-D1074.
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SVM-Prot 2016: a web-server for machine learning prediction of protein functional families from sequence irrespective of similarity
Published in PLoS ONE, 2016
This paper details major improvements to the SVM-Prot web-server, a machine learning tool for predicting protein functional families from sequences, complementing similarity-based methods.
Recommended citation: Li, Y. H., Xu, J. Y., Tao, L., Li, X. F., Li, S., Zeng, X., Chen, S. Y., Zhang, P., Qin, C., Zhang, C., Chen, Z., Zhu, F., & Chen, Y. Z. (2016). "SVM-Prot 2016: a web-server for machine learning prediction of protein functional families from sequence irrespective of similarity." PLoS ONE. 11(8):e0155290.
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The human kinome targeted by FDA approved multi-target drugs and combination products: a comparative study from the drug-target interaction network perspective
Published in PLoS ONE, 2016
This paper provides a comparative network analysis of FDA-approved multi-target drugs and combination products that target the human kinome, offering insights for next-generation polypharmacology.
Recommended citation: Li, Y. H., Wang, P. P., Li, X. X., Yu, C. Y., Yang, H., Zhou, J., Xue, W. W., Tan, J., & Zhu, F. (2016). "The human kinome targeted by FDA approved multi-target drugs and combination products: a comparative study from the drug-target interaction network perspective." PLoS ONE. 11(11):e0165737.
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Therapeutic target database update 2018: enriched resource for facilitating bench-to-clinic research of targeted therapeutics
Published in Nucleic Acids Research, 2018
This paper describes a major update to the Therapeutic Target Database (TTD), enhancing its utility for patient-focused research and clinical investigation of targeted therapeutics.
Recommended citation: Li, Y. H., Yu, C. Y., Li, X. X., Zhang, P., Tang, J., Yang, Q., Fu, T., Zhang, X., Cui, X., Tu, G., Zhang, Y., Li, S., Yang, F., Sun, Q., Qin, C., Zeng, X., Chen, Z., Chen, Y. Z., & Zhu, F. (2018). "Therapeutic target database update 2018: enriched resource for facilitating bench-to-clinic research of targeted therapeutics." Nucleic Acids Research. 46(D1):D1121-D1127.
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Clinical trials, progression-speed differentiating features, and swiftness rule of the innovative targets of first-in-class drugs
Published in Briefings in Bioinformatics, 2020
This paper analyzes the clinical trial timelines of 89 innovative targets of first-in-class drugs to identify features that differentiate the speed of clinical progression.
Recommended citation: Li, Y. H., Li, X. X., Hong, J. J., Wang, Y. X., Fu, J. B., Yang, H., Yu, C. Y., Li, F. C., Hu, J., Xue, W. W., Jiang, Y. Y., Chen, Y. Z., & Zhu, F. (2020). "Clinical trials, progression-speed differentiating features, and swiftness rule of the innovative targets of first-in-class drugs." Briefings in Bioinformatics. 21(2):649-662.
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Prediction of bitterant and sweetener using structure-taste relationship models based on an artificial neural network
Published in Food Research International, 2022
This work develops and compares three structure-taste relationship models based on artificial neural networks to predict whether a molecule is a bitterant, sweetener, or neither.
Recommended citation: Bo, W., Qin, D., Zheng, X., Wang, Y., Ding, B., Li, Y., & Liang, G. (2022). "Prediction of bitterant and sweetener using structure-taste relationship models based on an artificial neural network." Food Research International. 153:110974.
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A Comparative Benchmarking and Evaluation Framework for Heterogeneous Network-Based Drug Repositioning Methods
Published in Briefings in Bioinformatics, 2024
This paper presents a systematic benchmarking study of 28 heterogeneous network-based drug repositioning methods, providing a comprehensive framework to evaluate their performance, scalability, and usability.
Recommended citation: Li, Y., Yang, Y., Tong, Z. et al. (2024). "A Comparative Benchmarking and Evaluation Framework for Heterogeneous Network-Based Drug Repositioning Methods." Briefings in Bioinformatics. 25(3):bbae172.
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DTNPD: A comprehensive database of drugs and targets for neurological and psychiatric disorders
Published in Computers in Biology and Medicine, 2024
This paper introduces DTNPD, a specialized, comprehensive database of drugs and targets for neurological and psychiatric disorders (NPDs) to address data quality and coverage gaps in existing resources.
Recommended citation: Luo, D., Tong, Z., Wen, L., Bai, M., Jin, X., Liu, Z., Li, Y., & Xue, W. (2024). "DTNPD: A comprehensive database of drugs and targets for neurological and psychiatric disorders." Computers in Biology and Medicine. 175:108536.
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Systematic evaluation with practical guidelines for single-cell and spatially resolved transcriptomics data simulation under multiple scenarios
Published in Genome Biology, 2024
This paper presents a systematic evaluation of 49 simulation methods for single-cell RNA sequencing (scRNA-seq) and spatially resolved transcriptomics (SRT) data, providing practical guidelines for selecting appropriate simulators.
Recommended citation: Duo, H., Li, Y., Lan, Y. et al. (2024). "Systematic evaluation with practical guidelines for single-cell and spatially resolved transcriptomics data simulation under multiple scenarios." Genome Biology. 25:145.
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Adaptive multi-view learning method for enhanced drug repurposing using chemical-induced transcriptional profiles, knowledge graphs, and large language models
Published in Journal of Pharmaceutical Analysis, 2025
This study introduces adaptive multi-view learning (AMVL), a novel methodology that integrates chemical-induced transcriptional profiles, knowledge graph embeddings, and large language model representations to enhance drug repurposing predictions.
Recommended citation: Yan, Y., Yang, Y., Tong, Z., Wang, Y., Yang, F., Pan, Z., Liu, C., Bai, M., Xie, Y., Li, Y., Shu, K., & Li, Y. (2025). "Adaptive multi-view learning method for enhanced drug repurposing using chemical-induced transcriptional profiles, knowledge graphs, and large language models." Journal of Pharmaceutical Analysis, 15(6), 101275.
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Lung Cancer Biomarker Database (LCBD): A Comprehensive and Curated Repository of Lung Cancer Biomarkers
Published in BMC Cancer, 2025
This paper introduces the Lung Cancer Biomarker Database (LCBD), a centralized, curated platform designed to consolidate fragmented biomarker data to aid in early screening and personalized treatment of lung cancer.
Recommended citation: Li, Y., Tong, Z., Yang, Y. et al. (2025). "Lung Cancer Biomarker Database (LCBD): a comprehensive and curated repository of lung cancer biomarkers." BMC Cancer. 25:478.
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Efficient fine-tuning of small-parameter large language models for biomedical bilingual multi-task applications
Published in Applied Soft Computing, 2025
This study proposes an efficient fine-tuning framework for small-parameter large language models (LLMs) to handle biomedical bilingual multi-task applications, balancing performance with computational efficiency.
Recommended citation: Li, Y., Yan, Y., Tong, Z., Wang, Y., Yang, Y., Bai, M., Pu, D., Xie, J., Liu, C., Li, B., Liu, M., & Shu, K. (2025). "Efficient fine-tuning of small-parameter large language models for biomedical bilingual multi-task applications." Applied Soft Computing, 175, 113084.
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VARIDT 4.0: distribution variability of drug transporters
Published in Nucleic Acids Research (IF=13.1, CAS Ranking: Q2 Top), 2025
This paper introduces VARIDT 4.0, a database focused on the distribution variability of drug transporters, published in Nucleic Acids Research.
Recommended citation: Li, Y., Yang, F., Pan, Z., Yan, Y., Jiang, B., Huang, X., Wang, H., Qin, X., Zeng, S., Fu, T., & Zhu, F. (2025). "VARIDT 4.0: distribution variability of drug transporters." Nucleic Acids Research. Accepted.
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LKE-DTA: predicting drug–target binding affinity with large language model representations and knowledge graph embeddings
Published in Molecular Diversity, 2025
This work introduces LKE-DTA, a novel deep learning framework that synergistically integrates large language models (LLMs) with knowledge graphs (KGs) to create comprehensive multi-dimensional representations for drugs and proteins for drug-target binding affinity (DTA) prediction.
Recommended citation: Mou, J., Yan, Y., Jiang, B., Yang, F., Pan, Z., Huang, X., Bai, M., Han, Z., & Li, Y. (2025). "LKE-DTA: predicting drug–target binding affinity with large language model representations and knowledge graph embeddings." Molecular Diversity.
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talks
Talk 1 on Relevant Topic in Your Field
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Conference Proceeding talk 3 on Relevant Topic in Your Field
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teaching
生物信息学导论 (Introduction to Bioinformatics)
本科生课程, 重庆邮电大学, 生物信息学院, 2023
课程简介
本课程是生物信息学专业的入门核心课程，旨在帮助学生建立生物信息学的完整知识体系，为后续的专业课程学习和科研工作打下坚实的基础。
核心内容
- 基本概念: 生物信息学定义、发展历史与前沿领域。
- 生物数据库: 掌握NCBI, Ensembl, PDB等核心数据库的使用。
- 序列比对: 理解并应用BLAST, Smith-Waterman等经典算法。
- 基因与功能: 学习基因预测、功能注释的方法与工具。
- 蛋白质分析: 蛋白质结构与功能的预测方法。
- 进化分析: 系统发育分析与分子进化理论基础。
Python高级编程 (Advanced Python Programming)
本科生/研究生课程, 重庆邮电大学, 生物信息学院, 2024
课程简介
本课程面向已具备Python基础的学生，旨在全面提升其编程能力和解决复杂问题的效率，以应对生物信息学领域的数据密集型挑战。
核心内容
- 高级特性: 深入学习装饰器、生成器、元类等。
- 面向对象 (OOP): 掌握高级设计模式与应用。
- 并发编程: 包含多线程、多进程及异步IO模型。
- 科学计算: NumPy, Pandas, Matplotlib等库的高级用法。
- 性能优化: 学习代码分析、瓶颈定位与性能提升技巧。